rs11651617

Variant names:

• chr17-14507891-A-G
• rs11651617
• ENST00000700765.2:n.439-18294A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000700765.2(ENSG00000230647):​n.439-18294A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,762 control chromosomes in the GnomAD database, including 3,958 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (3958 hom., cov: 31)
• Consequence: ENSG00000230647 ENST00000700765.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 1 publications found

Genes affected

ENSG00000230647 (HGNC:58488):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230647	ENST00000700765.2	n.439-18294A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34558 AN: 151644 Hom.: 3960 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.222

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.228 AC: 34571 AN: 151762 Hom.: 3958 Cov.: 31 AF XY: 0.230 AC XY: 17081 AN XY: 74152

African (AFR) AF: 0.229 AC: 9478 AN: 41346

American (AMR) AF: 0.199 AC: 3030 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3466

East Asian (EAS) AF: 0.218 AC: 1115 AN: 5122

South Asian (SAS) AF: 0.216 AC: 1035 AN: 4798

European-Finnish (FIN) AF: 0.287 AC: 3022 AN: 10524

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15567 AN: 67936

Other (OTH) AF: 0.221 AC: 468 AN: 2114

Alfa AF: 0.228 Hom.: 2049

Bravo AF: 0.218

Asia WGS AF: 0.215 AC: 745 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.55
PhyloP100		-0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11651617; hg19: chr17-14411208; COSMIC: COSV60075454;